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Structure of the trimeric globular domain of Adiponectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DOU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 0.2 mM Li2SO4, 0.1 M sodium acetate pH 4.5, 50% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.01 38.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.923 α = 116.83 b = 49.635 β = 100.89 c = 50.306 γ = 104.92
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 0.989 50 95.6 0.134 0.155 0.997 5.01 3.95 199981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.99 1.05 92.9 1.545 0.248 0.32 3.909
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4DOU 0.99 40.768 1.96 198521 7658 92.26 0.1657 0.1653 0.1646 0.1895 0.1892 14.75
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3378 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing